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@ARTICLE{Agoncillo1999,
  author = {A. V. Agoncillo and J. L. Mejino and C. Rosse},
  title = {Influence of the Digital Anatomist Foundational Model on traditional
	representations of anatomical concepts.},
  journal = {Proc AMIA Symp},
  year = {1999},
  pages = {2--6},
  abstract = {A principled and logical representation of the structure of the human
	body has led to conflicts with traditional representations of the
	same knowledge by anatomy textbooks. The examples which illustrate
	resolution of these conflicts suggest that stricter requirements
	must be met for semantic consistency, expressivity and specificity
	by knowledge sources intended to support inference than by textbooks
	and term lists. These next-generation resources should influence
	traditional concept representation, rather than be constrained by
	convention.},
  institution = {Department of Biological Structure, University of Washington, School
	of Medicine, Seattle 98195, USA.},
  keywords = {Anatomy; Anatomy, Artistic; Humans; Medical Illustration; Models,
	Anatomic; Semantics; Terminology as Topic; Textbooks as Topic},
  owner = {olivier},
  pii = {D005834},
  pmid = {10566309},
  timestamp = {2009.07.16}
}

@INPROCEEDINGS{sofa,
  author = {J\'er\'emie Allard and St\'ephane Cotin and Fran\c{c}ois Faure and
	Pierre-Jean Bensoussan and Fran\c{c}ois Poyer and Christian Duriez
	and Herv\'e Delingette and Laurent Grisoni},
  title = {{SOFA} - an Open Source Framework for Medical Simulation},
  booktitle = {Medicine Meets Virtual Reality, MMVR 15, February, 2007},
  year = {2007},
  pages = {1--6},
  address = {Long Beach, California, USA},
  note = {\url{http://www.sofa-framework.org}}
}

@ARTICLE{Brinkley1999,
  author = {Brinkley, J.F. and Wong, B.A. and Hinshaw, K.P. and Rosse, C.},
  title = {Design of an anatomy information system},
  journal = IEEE_M_CGA,
  year = {1999},
  volume = {19},
  pages = {38--48},
  number = {3},
  doi = {10.1109/38.761548},
  issn = {0272-1716},
  keywords = {data visualisation, medical computing, medical information systems,
	physiology, Digital Anatomist Project, anatomical representation
	interaction, anatomy information system design, clinical medicine,
	education, graphics, structure-based information system, visualization},
  owner = {olivier},
  timestamp = {2009.07.16}
}

@INPROCEEDINGS{Cook2004,
  author = {Cook, D.L. and Mejino, J.L.V. and Rosse, C.},
  title = {The foundational model of anatomy: a template for the symbolic representation
	of multi-scale physiological functions},
  booktitle = {Proc. 26th Annual International Conference of the IEEE Engineering
	in Medicine and Biology Society IEMBS '04},
  year = {2004},
  volume = {2},
  pages = {5415--5418},
  doi = {10.1109/IEMBS.2004.1404513},
  keywords = {ontologies (artificial intelligence), physiological models, semantic
	networks, foundational model of anatomy, functional bioinformatics,
	human anatomy, knowledge representation, multiscale physiological
	functions, physiology reference ontology, semantic structure, Anatomy,
	Physiology Reference Ontology, Prot&amp, #233, g&amp, #233, -2000,
	informatics, ontology, physiology},
  owner = {olivier},
  timestamp = {2009.07.16}
}

@ARTICLE{Cook2004a,
  author = {D. L. Cook and J. L V Mejino and C. Rosse},
  title = {The foundational model of anatomy: a template for the symbolic representation
	of multi-scale physiological functions.},
  journal = {Conf Proc IEEE Eng Med Biol Soc},
  year = {2004},
  volume = {7},
  pages = {5415--5418},
  abstract = {We describe the foundational model of anatomy (FMA), reference ontology
	for the discipline of human anatomy. Using the semantic structure
	of the FMA as knowledge representation template, we propose a physiology
	reference ontology (PRO) as a corresponding ontology for "functional
	bioinformatics". We envision the PRO as a source vocabulary for building
	symbolic representations of human physiological states and actions
	that may ultimately be extensible to other species. We describe the
	evolving architecture of the PRO, in terms of simple examples based
	on the anatomical concepts encoded in the FMA.},
  doi = {10.1109/IEMBS.2004.1404513},
  institution = { Biophysics, Washington University, Seattle, WA, USA.},
  owner = {olivier},
  pmid = {17271570},
  timestamp = {2009.07.16},
  url = {http://dx.doi.org/10.1109/IEMBS.2004.1404513}
}

@ARTICLE{Cook2004b,
  author = {Daniel L Cook and Jose L V Mejino and Cornelius Rosse},
  title = {Evolution of a Foundational Model of Physiology: symbolic representation
	for functional bioinformatics.},
  journal = {Stud Health Technol Inform},
  year = {2004},
  volume = {107},
  pages = {336--340},
  number = {Pt 1},
  abstract = {We describe the need for a Foundational Model of Physiology (FMP)
	as a reference ontology for "functional bioinformatics". The FMP
	is intended to support symbolic lookup, logical inference and mathematical
	analysis by integrating descriptive, qualitative and quantitative
	functional knowledge. The FMP will serve as a symbolic representation
	of biological functions initially pertaining to human physiology
	and ultimately extensible to other species. We describe the evolving
	architecture of the FMP, which is based on the ontological principles
	of the BioD biological description language and the Foundational
	Model of Anatomy (FMA).},
  institution = {Structural Informatics Group, University of Washington, Seattle,
	WA, USA. raintown@halcyon.com},
  keywords = {Computational Biology; Humans; Models, Biological; Physiology; Vocabulary,
	Controlled},
  owner = {olivier},
  pii = {D040005412},
  pmid = {15360830},
  timestamp = {2009.07.16}
}

@ARTICLE{Detwiler2004,
  author = {Landon T Detwiler and Emily Chung and Ann Li and José L V Mejino
	and Augusto Agoncillo and James Brinkley and Cornelius Rosse and
	Linda Shapiro},
  title = {A relation-centric query engine for the Foundational Model of Anatomy.},
  journal = {Stud Health Technol Inform},
  year = {2004},
  volume = {107},
  pages = {341--345},
  number = {Pt 1},
  abstract = {The Foundational Model of Anatomy (FMA), a detailed representation
	of the structural organization of the human body, was constructed
	to support the development of software applications requiring knowledge
	of anatomy. The FMA's focus on the structural relationships between
	anatomical entities distinguishes it from other current anatomical
	knowledge sources. We developed Emily, a query engine for the FMA,
	to enable users to explore the richness and depth of these relationships.
	Preliminary analysis suggests that Emily is capable of correctly
	processing real world anatomical queries provided they have been
	translated into a constrained form suitable for processing by the
	query engine.},
  institution = {Structural Informatics Group, University of Washington, Seattle,
	WA 98195, USA.},
  keywords = {Anatomy; Artificial Intelligence; Humans; Information Storage and
	Retrieval; Models, Anatomic; User-Computer Interface; Vocabulary,
	Controlled},
  owner = {olivier},
  pii = {D040004345},
  pmid = {15360831},
  timestamp = {2009.07.16}
}

@ARTICLE{Martin2001,
  author = {R. F. Martin and J. L. Mejino and D. M. Bowden and J. F. Brinkley
	and C. Rosse},
  title = {Foundational model of neuroanatomy: implications for the Human Brain
	Project.},
  journal = {Proc AMIA Symp},
  year = {2001},
  pages = {438--442},
  abstract = {In order to meet the need for a controlled terminology in neuroinformatics,
	we have integrated the extensive terminology of NeuroNames into the
	Foundational Model of anatomy. We illustrate the application of foundational
	principles for the establishment of an inheritance hierarchy, which
	accommodates anatomical attributes of neuroanatomical concepts and
	provides the foundation to which other information may be linked.},
  institution = {nformatics Group, Department of Biological Structure and Regional
	Primate Research Center, University of Washington, Seattle, WA 98195,
	USA.},
  keywords = {Brain; Databases as Topic; Humans; Neuroanatomy; Terminology as Topic;
	Vocabulary, Controlled},
  owner = {olivier},
  pii = {D010001583},
  pmid = {11825226},
  timestamp = {2009.07.16}
}

@ARTICLE{Martin2003,
  author = {Richard F Martin and Kurt Rickard and José L V Mejino and Augusto
	V Agoncillo and James F Brinkley and Cornelius Rosse and Structural
	Informatics Group},
  title = {The evolving neuroanatomical component of the Foundational Model
	of Anatomy.},
  journal = {AMIA Annu Symp Proc},
  year = {2003},
  pages = {927},
  abstract = {In order to meet the need for an expressive ontology in neuroinformatics,
	we have integrated the extensive terminologies of NeuroNames and
	Terminologia Anatomica into the Foundational Model of Anatomy (FMA).
	We have enhanced the FMA to accommodate information unique to neuronal
	structures, such as axonal input/output relationships.},
  institution = {.},
  keywords = {Anatomy; Humans; Neuroanatomy; Unified Medical Language System; Vocabulary,
	Controlled},
  owner = {olivier},
  pmid = {14728433},
  timestamp = {2009.07.16}
}

@ARTICLE{Mejino1999,
  author = {J. L. Mejino and C. Rosse},
  title = {Conceptualization of anatomical spatial entities in the Digital Anatomist
	Foundational Model.},
  journal = {Proc AMIA Symp},
  year = {1999},
  pages = {112--116},
  abstract = {Anatomical spatial concepts are indispensable in educational and clinical
	discourse, yet a system for representing these concepts has not been
	proposed. Guided by explicit principles and definitions of the Digital
	Anatomist Foundational Model, we developed an ontology of spaces,
	surfaces, lines and points that are associated with anatomical structures.
	Ontologies for Anatomical Structure and Anatomical Spatial Entity
	were instantiated for the thorax, abdomen, pelvis and perineum. Representing
	the concepts in--part of--hierarchies as well, provided formative
	evaluation of the classification. We invite empirical evaluation
	of the Foundational Model through its use for educational and clinical
	applications.},
  institution = {Department of Biological Structure, University of Washington School
	of Medicine, Seattle 98195, USA.},
  keywords = {Anatomy; Humans; Models, Anatomic; Terminology as Topic; Vocabulary,
	Controlled},
  owner = {olivier},
  pii = {D005410},
  pmid = {10566331},
  timestamp = {2009.07.16}
}

@ARTICLE{Mejino2003,
  author = {José V Mejino and Augusto V Agoncillo and Kurt L Rickard and Cornelius
	Rosse},
  title = {Representing complexity in part-whole relationships within the Foundational
	Model of Anatomy.},
  journal = {AMIA Annu Symp Proc},
  year = {2003},
  pages = {450--454},
  keywords = {Anatomy; Humans; Models, Anatomic; Vocabulary, Controlled},
  owner = {olivier},
  pii = {D030002797},
  pmid = {14728213},
  timestamp = {2009.07.16}
}

@ARTICLE{Michael2001,
  author = {J. Michael and J. L. Mejino and C. Rosse},
  title = {The role of definitions in biomedical concept representation.},
  journal = {Proc AMIA Symp},
  year = {2001},
  pages = {463--467},
  abstract = {The Foundational Model (FM) of anatomy, developed as an anatomical
	enhancement of UMLS, classifies anatomical entities in a structural
	context. Explicit definitions have played a critical role in the
	establishment of FM classes. Essential structural properties that
	distinguish a group of anatomical entities serve as the differentiate
	for defining classes. These, as well as other structural attributes,
	are introduced as template slots in Protégé, a frame-based knowledge
	acquisition system, and are inherited by descendants of the class.
	A set of desiderata has evolved during the instantiation of the FM
	for formulating definitions. We contend that 1. these desiderata
	generalize to non-anatomical domains and 2. satisfying them in constituent
	vocabularies of UMLS would enhance the quality of information retrievable
	through UMLS.},
  institution = {Biological Structure, University of Washington, Seattle, WA, USA.},
  keywords = {Anatomy; Artificial Intelligence; Dictionaries as Topic; Humans; Semantics;
	Terminology as Topic; Unified Medical Language System; Vocabulary,
	Controlled},
  owner = {olivier},
  pii = {D010001637},
  pmid = {11825231},
  timestamp = {2009.07.16}
}

@ARTICLE{A-NesKryJerFau09,
  author = {Matthieu Nesme and Paul Kry and Lenka {Je\v{r}\'abkov\'a} and Fran\c{c}ois
	Faure},
  title = {Preserving Topology and Elasticity for Embedded Deformable Models},
  journal = {ACM Trans. Graph.},
  year = {2009},
  month = aou,
  note = {Proceedings of SIGGRAPH'09}
}

@ARTICLE{Rickard2004,
  author = {Kurt L Rickard and José L V Mejino and Richard F Martin and Augusto
	V Agoncillo and Cornelius Rosse},
  title = {Problems and solutions with integrating terminologies into evolving
	knowledge bases.},
  journal = {Stud Health Technol Inform},
  year = {2004},
  volume = {107},
  pages = {420--424},
  number = {Pt 1},
  abstract = {We have merged two established anatomical terminologies with an evolving
	ontology of biological structure: the Foundational Model of Anatomy.
	We describe the problems we have encountered and the solutions we
	have developed. We believe that both the problems and solutions generalize
	to the integration of any legacy terminology with a disciplined ontology
	within the same domain.},
  institution = {Structural Informatics Group, Department of Biological Structure,
	University of Washington, Seattle, WA 98195, USA.},
  keywords = {Anatomy; Eponyms; Female; Humans; Language; Male; Neuroanatomy; Software;
	Terminology as Topic; User-Computer Interface; Vocabulary, Controlled},
  owner = {olivier},
  pii = {D040003937},
  pmid = {15360847},
  timestamp = {2009.07.16}
}

@ARTICLE{Rosse2005,
  author = {Cornelius Rosse and Anand Kumar and Jose L V Mejino and Daniel L
	Cook and Landon T Detwiler and Barry Smith},
  title = {A strategy for improving and integrating biomedical ontologies.},
  journal = {AMIA Annu Symp Proc},
  year = {2005},
  pages = {639--643},
  abstract = {The integration of biomedical terminologies is indispensable to the
	process of information integration. When terminologies are linked
	merely through the alignment of their leaf terms, however, differences
	in context and ontological structure are ignored. Making use of the
	SNAP and SPAN ontologies, we show how three reference domain ontologies
	can be integrated at a higher level, through what we shall call the
	OBR framework (for: Ontology of Biomedical Reality). OBR is designed
	to facilitate inference across the boundaries of domain ontologies
	in anatomy, physiology and pathology.},
  institution = {Structural Informatics Group, Department of Biological Structure,
	University of Washington, USA.},
  keywords = {Anatomy; Humans; Pathology; Physiology; Terminology as Topic; Vocabulary,
	Controlled},
  owner = {olivier},
  pii = {58545},
  pmid = {16779118},
  timestamp = {2009.07.16}
}

@ARTICLE{Rosse1998,
  author = {C. Rosse and J. L. Mejino and B. R. Modayur and R. Jakobovits and
	K. P. Hinshaw and J. F. Brinkley},
  title = {Motivation and organizational principles for anatomical knowledge
	representation: the digital anatomist symbolic knowledge base.},
  journal = {J Am Med Inform Assoc},
  year = {1998},
  volume = {5},
  pages = {17--40},
  number = {1},
  abstract = {OBJECTIVE: Conceptualization of the physical objects and spaces that
	constitute the human body at the macroscopic level of organization,
	specified as a machine-parseable ontology that, in its human-readable
	form, is comprehensible to both expert and novice users of anatomical
	information. DESIGN: Conceived as an anatomical enhancement of the
	UMLS Semantic Network and Metathesaurus, the anatomical ontology
	was formulated by specifying defining attributes and differentia
	for classes and subclasses of physical anatomical entities based
	on their partitive and spatial relationships. The validity of the
	classification was assessed by instantiating the ontology for the
	thorax. Several transitive relationships were used for symbolically
	modeling aspects of the physical organization of the thorax. RESULTS:
	By declaring Organ as the macroscopic organizational unit of the
	body, and defining the entities that constitute organs and higher
	level entities constituted by organs, all anatomical entities could
	be assigned to one of three top level classes (Anatomical structure,
	Anatomical spatial entity and Body substance). The ontology accommodates
	both the systemic and regional (topographical) views of anatomy,
	as well as diverse clinical naming conventions of anatomical entities.
	CONCLUSIONS: The ontology formulated for the thorax is extendible
	to microscopic and cellular levels, as well as to other body parts,
	in that its classes subsume essentially all anatomical entities that
	constitute the body. Explicit definitions of these entities and their
	relationships provide the first requirement for standards in anatomical
	concept representation. Conceived from an anatomical viewpoint, the
	ontology can be generalized and mapped to other biomedical domains
	and problem solving tasks that require anatomical knowledge.},
  institution = {Department of Biological Structure, University of Washington, Seattle
	98195, USA. rosse@u.washington.edu},
  keywords = {Anatomy; Artificial Intelligence; Humans; Semantics; Terminology as
	Topic; Thorax; Unified Medical Language System; Vocabulary, Controlled},
  owner = {olivier},
  pmid = {9452983},
  timestamp = {2009.07.16}
}

@ARTICLE{Rosse2003,
  author = {Cornelius Rosse and José L V Mejino},
  title = {A reference ontology for biomedical informatics: the Foundational
	Model of Anatomy.},
  journal = {J Biomed Inform},
  year = {2003},
  volume = {36},
  pages = {478--500},
  number = {6},
  month = {Dec},
  abstract = {The Foundational Model of Anatomy (FMA), initially developed as an
	enhancement of the anatomical content of UMLS, is a domain ontology
	of the concepts and relationships that pertain to the structural
	organization of the human body. It encompasses the material objects
	from the molecular to the macroscopic levels that constitute the
	body and associates with them non-material entities (spaces, surfaces,
	lines, and points) required for describing structural relationships.
	The disciplined modeling approach employed for the development of
	the FMA relies on a set of declared principles, high level schemes,
	Aristotelian definitions and a frame-based authoring environment.
	We propose the FMA as a reference ontology in biomedical informatics
	for correlating different views of anatomy, aligning existing and
	emerging ontologies in bioinformatics ontologies and providing a
	structure-based template for representing biological functions.},
  doi = {10.1016/j.jbi.2003.11.007},
  institution = { Biomedical Informatics, Structural Informatics Group, University
	of Washington, Seattle, WA 98195, USA. rosse@u.washington.edu},
  keywords = {Abstracting and Indexing as Topic; Algorithms; Anatomy; Artificial
	Intelligence; Computational Biology; Database Management Systems;
	Databases, Factual; Humans; Information Storage and Retrieval; Linguistics;
	Models, Anatomic; National Library of Medicine (U.S.); Natural Language
	Processing; Semantics; Subject Headings; Terminology as Topic; Unified
	Medical Language System; United States; Vocabulary, Controlled},
  owner = {olivier},
  pii = {S1532046403001278},
  pmid = {14759820},
  timestamp = {2009.07.16},
  url = {http://dx.doi.org/10.1016/j.jbi.2003.11.007}
}

@ARTICLE{A-WonRosBri99,
  author = {B.A. Wong and C. Rosse and J.F. Brinkley},
  title = {Semi-automatic Scene Generation using the Digital Anatomist Foundational
	Model},
  journal = {J. Am. Med. Assoc.},
  year = {1999},
  volume = {AMIA '99 Symp.},
  pages = {637-641},
  note = {Suppl.}
}

@MISC{blender,
  note = {\url{http://www.blender.org}}
}

